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A structure pattern filter for atom-atom maps.
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tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsAtomAtomMapFilter.java
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/* | ||
* Copyright (c) 2016 John May <jwmay@users.sf.net> | ||
* | ||
* Contact: cdk-devel@lists.sourceforge.net | ||
* | ||
* This program is free software; you can redistribute it and/or modify it | ||
* under the terms of the GNU Lesser General Public License as published by | ||
* the Free Software Foundation; either version 2.1 of the License, or (at | ||
* your option) any later version. All we ask is that proper credit is given | ||
* for our work, which includes - but is not limited to - adding the above | ||
* copyright notice to the beginning of your source code files, and to any | ||
* copyright notice that you may distribute with programs based on this work. | ||
* | ||
* This program is distributed in the hope that it will be useful, but WITHOUT | ||
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or | ||
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public | ||
* License for more details. | ||
* | ||
* You should have received a copy of the GNU Lesser General Public License | ||
* along with this program; if not, write to the Free Software | ||
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U | ||
*/ | ||
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package org.openscience.cdk.smiles.smarts; | ||
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import com.google.common.base.Predicate; | ||
import com.google.common.collect.ArrayListMultimap; | ||
import com.google.common.collect.Multimap; | ||
import com.google.common.primitives.Ints; | ||
import org.openscience.cdk.CDKConstants; | ||
import org.openscience.cdk.ReactionRole; | ||
import org.openscience.cdk.interfaces.IAtom; | ||
import org.openscience.cdk.interfaces.IAtomContainer; | ||
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import java.util.ArrayList; | ||
import java.util.Arrays; | ||
import java.util.Collection; | ||
import java.util.HashSet; | ||
import java.util.List; | ||
import java.util.Map; | ||
import java.util.Set; | ||
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/** | ||
* A filter for substructure matches implementing the logic for Atom-Atom Mapping matching. The following | ||
* table from the Daylight theory manual summarises the expected functionality: | ||
* | ||
* <pre> | ||
* C>>C CC>>CC 4 hits No maps, normal match. | ||
* C>>C [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits No maps in query, maps in target are ignored. | ||
* [C:1]>>C [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits Unpaired map in query ignored. | ||
* [C:1]>>[C:1] CC>>CC 0 hits No maps in target, hence no matches. | ||
* [C:?1]>>[C:?1] CC>>CC 4 hits Query says mapped as shown or not present. | ||
* [C:1]>>[C:1] [CH3:7][CH3:8]>>[CH3:7][CH3:8] 2 hits Matches for target 7,7 and 8,8 atom pairs. | ||
* [C:1]>>[C:2] [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits When a query class is not found on both sides of the | ||
* query, it is ignored; this query does NOT say that the | ||
* atoms are in different classes. | ||
* [C:1][C:1]>>[C:1] [CH3:7][CH3:7]>>[CH3:7][CH3:7] 4 hits Atom maps match with "or" logic. All atoms get bound to | ||
* class 7. | ||
* [C:1][C:1]>>[C:1] [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits The reactant atoms are bound to classes 7 and 8. Note that | ||
* having the first query atom bound to class 7 does not | ||
* preclude binding the second atom. Next, the product | ||
* atom can bind to classes 7 or 8. | ||
* [C:1][C:1]>>[C:1] [CH3:7][CH3:7]>>[CH3:7][CH3:8] 2 hits The reactants are bound to class 7. The product atom can | ||
* bind to class 7 only. | ||
* </pre> | ||
* | ||
* @see <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight Theory Manual</a> | ||
*/ | ||
final class SmartsAtomAtomMapFilter implements Predicate<int[]> { | ||
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private final List<MappedPairs> mapped = new ArrayList<>(); | ||
private final IAtomContainer target; | ||
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SmartsAtomAtomMapFilter(IAtomContainer query, IAtomContainer target) { | ||
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Multimap<Integer,Integer> reactInvMap = null; | ||
Multimap<Integer,Integer> prodInvMap = null; | ||
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this.target = target; | ||
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// transform query maps in to matchable data-structure | ||
final int numAtoms = query.getAtomCount(); | ||
for (int idx = 0; idx < numAtoms; idx++) { | ||
IAtom atom = query.getAtom(idx); | ||
final int mapidx = mapidx(atom); | ||
if (mapidx == 0) continue; | ||
switch (role(atom)) { | ||
case Reactant: | ||
if (reactInvMap == null) reactInvMap = ArrayListMultimap.create(); | ||
reactInvMap.put(mapidx, idx); | ||
break; | ||
case Product: | ||
if (prodInvMap == null) prodInvMap = ArrayListMultimap.create(); | ||
prodInvMap.put(mapidx, idx); | ||
break; | ||
} | ||
} | ||
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if (reactInvMap != null && prodInvMap != null) { | ||
for (Map.Entry<Integer, Collection<Integer>> e : reactInvMap.asMap().entrySet()) { | ||
int[] reacMaps = Ints.toArray(e.getValue()); | ||
int[] prodMaps = Ints.toArray(prodInvMap.get(e.getKey())); | ||
if (prodMaps.length == 0) | ||
continue; // unpaired | ||
mapped.add(new MappedPairs(reacMaps, prodMaps)); | ||
} | ||
} | ||
} | ||
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/** | ||
* Safely access the mapidx of an atom, returns 0 if null. | ||
* | ||
* @param atom atom | ||
* @return mapidx, 0 if undefined | ||
*/ | ||
private int mapidx(IAtom atom) { | ||
Integer mapidx = atom.getProperty(CDKConstants.ATOM_ATOM_MAPPING); | ||
if (mapidx != null) | ||
return mapidx; | ||
return 0; | ||
} | ||
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/** | ||
* Safely access the reaction role of an atom, returns {@link ReactionRole#None} if null. | ||
* | ||
* @param atom atom | ||
* @return mapidx, None if undefined | ||
*/ | ||
private ReactionRole role(IAtom atom) { | ||
ReactionRole role = atom.getProperty(CDKConstants.REACTION_ROLE); | ||
if (role != null) | ||
return role; | ||
return ReactionRole.None; | ||
} | ||
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/** | ||
* Filters a structure match (described as an index permutation query -> target) for | ||
* those where the atom-atom maps are acceptable. | ||
* | ||
* @param perm permuation | ||
* @return whether the match should be accepted | ||
*/ | ||
@Override | ||
public boolean apply(int[] perm) { | ||
for (MappedPairs mpair : mapped) { | ||
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// possibly 'or' of query maps, need to use a set | ||
if (mpair.rIdxs.length > 1) { | ||
// bind target reactant maps | ||
final Set<Integer> bound = new HashSet<>(); | ||
for (int rIdx : mpair.rIdxs) { | ||
int refidx = mapidx(target.getAtom(perm[rIdx])); | ||
if (refidx == 0) return false; // unmapped in target | ||
bound.add(refidx); | ||
} | ||
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// check product maps | ||
for (int pIdx : mpair.pIdxs) { | ||
if (!bound.contains(mapidx(target.getAtom(perm[pIdx])))) | ||
return false; | ||
} | ||
} | ||
// no 'or' of query atom map (more common case) | ||
else { | ||
final int refidx = mapidx(target.getAtom(perm[mpair.rIdxs[0]])); | ||
if (refidx == 0) return false; // unmapped in target | ||
// pairwise mismatch | ||
if (refidx != mapidx(target.getAtom(perm[mpair.pIdxs[0]]))) | ||
return false; | ||
for (int i = 1; i < mpair.pIdxs.length; i++) { | ||
if (refidx != mapidx(target.getAtom(perm[mpair.pIdxs[i]]))) | ||
return false; | ||
} | ||
} | ||
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} | ||
return true; | ||
} | ||
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/** | ||
* Helper class list all reactant atom indices (rIdxs) and product | ||
* atom indices (pIdxs) that are in the same Atom-Atom-Mapping class. | ||
*/ | ||
private final class MappedPairs { | ||
final int[] rIdxs, pIdxs; | ||
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private MappedPairs(int[] rIdxs, int[] pIdxs) { | ||
this.rIdxs = rIdxs; | ||
this.pIdxs = pIdxs; | ||
} | ||
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@Override | ||
public String toString() { | ||
return "{" + Arrays.toString(rIdxs) + "=>" + Arrays.toString(pIdxs) + "}"; | ||
} | ||
} | ||
} |
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